Hello list, I tried out the Membrane Builder at www.charmm-gui.org, which generates CHARMM input files for a combinded membrane-protein system and it looks quite good. The conversion CHARMM -> GROMACS is a bit tricky, I know, but I wanted to try it, though:
Using the Perl script on http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,59/ I converted the CHARMM force field par_all27_prot_lipid.prm (found at http://mackerell.umaryland.edu/CHARMM_ff_params.html) to a GROMACS-like .itp file. I used the files of http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz (containing amongst others ffcharmm.itp and ffcharmm.rtp), so -ff charmm is available in pdb2gmx. (According to the readme file, now it should be possible to execute pdb2gmx and create a .top file, that has to be modified further by charmm27-run-addtop-gromacs-dihe.sh, also included in this tar.gz.) When I tried to execute pdb2gmx -ignh -ff charmm -f usedfile.pdb -o usedfile_new.pdb -p usedfile_new.top -ter I got some errors first because of the terminal database files ffcharmm-c.tdb and ffcharmm-n.tdb, which had to be edited (simply remove some columns, then it works). But now I can't find out how to handle "Fatal Error: Atom CD in residue ILE 1 not found in rtp enrty with 19 atoms while sorting atoms" Sorry for that long mail, but to make the problem clear, here are parts cited from the used files: ffcharmm.rtp --------------------------------------------------------------------------------------------- [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl 1 1 3 1 1 3 . . . [ ILE ] [ atoms ] N NH1 -0.470 1 H H 0.310 1 CA CT1 0.070 1 HA HB 0.090 1 CB CT1 -0.090 2 HB HA 0.090 2 CG2 CT3 -0.270 3 HG21 HA 0.090 3 HG22 HA 0.090 3 HG23 HA 0.090 3 CG1 CT2 -0.180 4 HG11 HA 0.090 4 HG12 HA 0.090 4 CD1 CT3 -0.270 5 HD11 HA 0.090 5 HD12 HA 0.090 5 HD13 HA 0.090 5 C C 0.510 6 O O -0.510 6 [ bonds ] CB CA CG1 CB CG2 CB CD1 CG1 N H N CA C CA C +N CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 CG2 HG22 CG2 HG23 CD1 HD11 CD1 HD12 CD1 HD13 O C [ impropers ] N -C CA H improper_NH1_X_X_H_ C CA +N O improper_O_X_X_C_ . . . --------------------------------------------------------------------------------------------- used.pdb --------------------------------------------------------------------------------------------- REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) ON JUL, 04. 2008. REMARK ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER, PROTEIN, PORE WATER, REMARK DATE: 7/ 4/ 8 1:54: 9 CREATED BY USER: apache ATOM 1 N ILE 046 -5.242 -23.250 10.686 1.00 0.00 PROA ATOM 2 HT1 ILE 046 -4.310 -23.370 11.132 1.00 0.00 PROA ATOM 3 HT2 ILE 046 -5.645 -24.184 10.470 1.00 0.00 PROA ATOM 4 HT3 ILE 046 -5.874 -22.742 11.337 1.00 0.00 PROA ATOM 5 CA ILE 046 -5.098 -22.491 9.461 1.00 0.00 PROA ATOM 6 HA ILE 046 -4.770 -21.491 9.715 1.00 0.00 PROA ATOM 7 CB ILE 046 -4.187 -23.220 8.460 1.00 0.00 PROA ATOM 8 HB ILE 046 -4.600 -24.259 8.411 1.00 0.00 PROA ATOM 9 CG2 ILE 046 -4.198 -22.499 7.121 1.00 0.00 PROA ATOM 10 HG21 ILE 046 -3.671 -23.099 6.350 1.00 0.00 PROA ATOM 11 HG22 ILE 046 -5.238 -22.335 6.768 1.00 0.00 PROA ATOM 12 HG23 ILE 046 -3.694 -21.512 7.197 1.00 0.00 PROA ATOM 13 CG1 ILE 046 -2.758 -23.330 9.028 1.00 0.00 PROA ATOM 14 HG11 ILE 046 -2.272 -22.329 9.022 1.00 0.00 PROA ATOM 15 HG12 ILE 046 -2.817 -23.661 10.090 1.00 0.00 PROA ATOM 16 CD ILE 046 -1.847 -24.309 8.292 1.00 0.00 PROA ATOM 17 HD1 ILE 046 -0.859 -24.371 8.798 1.00 0.00 PROA ATOM 18 HD2 ILE 046 -2.295 -25.326 8.277 1.00 0.00 PROA ATOM 19 HD3 ILE 046 -1.677 -23.984 7.244 1.00 0.00 PROA ATOM 20 C ILE 046 -6.487 -22.360 8.876 1.00 0.00 PROA ATOM 21 O ILE 046 -6.913 -21.277 8.501 1.00 0.00 PROA ATOM 22 N LYS 047 -7.199 -23.476 8.826 1.00 0.00 PROA ATOM 23 HN LYS 047 -6.862 -24.356 9.156 1.00 0.00 PROA ATOM 24 CA LYS 047 -8.547 -23.497 8.277 1.00 0.00 PROA ATOM 25 HA LYS 047 -8.620 -22.640 7.618 1.00 0.00 PROA ATOM 26 CB LYS 047 -8.783 -24.823 7.551 1.00 0.00 PROA ATOM 27 HB1 LYS 047 -8.548 -25.639 8.273 1.00 0.00 PROA ATOM 28 HB2 LYS 047 -9.866 -24.918 7.313 1.00 0.00 PROA . . . --------------------------------------------------------------------------------------------- OK, the 21 lines in .pdb will hardly fit the 19 lines in .rtp, and the easiest solution might be to edit the .rtp file, but everything I tried so far failed, as I'm not too familiar with GROMACS. Hope you know a possibile solution, thanks in advance! Enjoy your weekend, best Volker -- ################################### Volker Wirth Center for Medical Physics and Technology Biophysics Group FAU Erlangen-Nuremberg Email: vwirth%at%biomed.uni-erlangen.de ################################### _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
